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energy_data.nonbonded_sel_atoms -- control interaction with picked atoms

Description:
When only a subset of all atoms is selected by the model.pick_atoms() or model.pick_hot_atoms() commands (set 1), this variable controls the interaction between the picked atoms and the rest of the system. When it is 2 (default), the non-bonded pairs will contain only selected atoms (set 1). This means that the optimized atoms will not ``feel'' the rest of the protein through the non-bonded terms at all.

If energy_data.nonbonded_sel_atoms is 1, only one of the atoms in the non-bonded pair has to be a selected atom. This means that the selected region feels the rest of the system through the non-bonded terms, at the expense of longer CPU times. When all atoms are selected, this variable has no effect.



Ben Webb 2005-06-20